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<h2>Changing the View</h2>

The software provides a number of options that control the display of
embeddings in PyMol. These are accessible via checkboxes at the top of
the results tree:
<ol>

<li><b>Show Protein?:</b> if this is checked, the protein structure
will be displayed along with each embedding and the reference
molecule.

<li><b>Show Neighborhood?:</b>
when checked, this causes the surface of the protein around the
reference molecule to be displayed.
This option is disabled unless <tt>Show Protein?</tt> is checked.

<li><b>Show H Bonds:</b>
when checked, this causes likely hydrogen bonds between the aligned
embedding and the protein to be drawn.


<li><b>Show Collisions:</b>
when checked, this causes close contacts between the 
embedding and the protein to be drawn.

</ol>

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